I just want to point out that Terry at least had legitimate reasons for why Batman never knew about him. I've yet to hear a single justification for how the World's Greatest Detective never noticed Talia being pregnant at any point, nor that her kid was his until years later. That's the sort of thing a paranoid bastard like Batman should have figured out a long time ago. Like I said, Terry at least made sense because Bruce didn't interact with Waller or Cadmus nearly as often as he did with Talia, so them managing to keep a cloning project secret from him is at least feasible. And, like Waller said, getting Bruce's DNA was frighteningly easy since he left it all over the place fighting battles as Batman.

That actually makes me theorize that Gordon does know Batman's identity and has since the beginning. I mean if Cadmus can collect Batman's DNA and identify it so easily then surely the GCPD could as well. I suspect Gordon kept the secret because all the good Batman does makes it worth breaking a rule or two to cover for him. And of course there's that Animated Series episode "Freefall" where Barbara is "killed" by Scarecrow and Gordon just instantly figures out Batman's identity? Nope, I say he knew all along but Babs dying was where he drew the line in covering it up.